Hello,

Thank you Michael for your input.  My feeling was that surface area would scale with ICV.  In any case, is there any recommendation on how to normalize the Jacobian?  My other ramble is that since it is already mapped into a common space, would I normalize the Jacobian, or would I have to normalize its precurser (surface area) measurement and then re-calculate the Jacobian?  My last ramble is that since the Jacobian is non-linear, is it possible to normalize it in a simple linear manner, or would it be a more complicated non-linear normalization?

I hope that makes sense.  Any feedback would be very greatly helpful!  Mahalo,

Jeff

Hi Jeff,
I'm confused here.  ICV and surface area are two very different things.

cheers,
-MH 

On Thu, Apr 12, 2012 at 12:06 PM, Jeff Sadino <jsadino.queens@gmail.com> wrote:

Thank you everyone for your great input.  After reading through all of the suggestions and references, I like the idea of using ICV rather than global averages, at least for this current study.  However, I do have one more question.  All the papers normalize on surface area.  If we want to present the Jacobian values, does it make sense to normalize the Jacobian values to the ICV?  Or are the Jacobians conceptionally too different from surface areas to do this?

Thank you,
Jeff

On Fri, Mar 23, 2012 at 1:29 AM, Michael Harms <mharms@conte.wustl.edu> wrote:

Our reply to that is here
http://bjp.rcpsych.org/content/196/5/414.2.long

which reminded me of other papers that have also used a global thickness
measure to covary for mean cortical thickness and thereby "address whether
any regional thickness differences were in excess of global cortical
thickness differences between groups" -- see references [1,4] in our
Reply.

cheers,
-MH

> Hi Michael and others,
>
> maybe it's this one:
>
> http://bjp.rcpsych.org/content/196/5/414.1.long
>
> best,
> -joost
>
>
> On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms
> <mharms@conte.wustl.edu>wrote:
>
>>
>> Hi Jeff,
>> I personally like the idea of using average thickness as a covariate to
>> control for a reduction in "whole brain" thickness, and have used that
>> approach in a paper.  If the Abstract that you mentioned indicated that
>> this is flawed, I'd be curious to know what the reason was...
>>
>> cheers,
>> -MH
>>
>> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
>> > Hi Jeff
>> >
>> > yes, I think this is still our recommendation for thickness, although
>> > perhaps David Salat can verify. As far as surface area, you might get
>> > Anderson Winkler to send you a preprint of his newly accepted paper on
>> > surface area comparisons and how to do them properly. I would have
>> said
>> > normalize by the 2/3 root of ICV (maybe David can comment on this as
>> well)
>> >
>> > cheers
>> > Bruce
>> >
>> >
>> > On Thu, 22 Mar 2012, Jeff Sadino wrote:
>> >
>> > > Hello,
>> > > For cortical thickness normalizations, Bruce said not to normalize
>> based on a HBM
>> > > abstract
>> > > (
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html).
>>  Is
>> > > this still the consensus?
>> > >
>> > > For cortical volume, it is pretty standard to normalize to eTIV.
>> > >
>> > > For cortical surface area (jacobian), I couldn't find any
>> information
>> on the wiki.
>> > >  Does anyone have any recommendations?
>> > >
>> > > Thank you,
>> > > Jeff
>> > >
>> > >
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